def test_cart2frac_traj(): nstep = 100 coords = rand(nstep,20,3) coords_copy = coords.copy() cell = rand(nstep,3,3) c1 = np.array([np.dot(coords[ii,...], np.linalg.inv(cell[ii,...])) for ii in \ range(nstep)]) c2 = _flib.cart2frac_traj(coords, cell) c3 = crys.coord_trans3d(coords, new=cell, old=num.extend_array(np.identity(3), nstep=nstep, axis=0)) assert (coords == coords_copy).all() assert np.allclose(c1, c2) assert np.allclose(c1, c3) assert c2.flags.f_contiguous
def test_frac2cart_traj(): nstep = 100 coords_frac = rand(nstep,20,3) coords_frac_copy = coords_frac.copy() cell = rand(nstep,3,3) c1 = np.array([np.dot(coords_frac[ii,...], cell[ii,...]) for ii in \ range(nstep)]) c2 = _flib.frac2cart_traj(coords_frac, cell) c3 = crys.coord_trans3d(coords_frac, old=cell, new=num.extend_array(np.identity(3), nstep=nstep, axis=0)) assert (coords_frac == coords_frac_copy).all() assert np.allclose(c1, c2) assert np.allclose(c1, c3) assert c2.flags.f_contiguous
def test_cart2frac_traj(): nstep = 100 coords = rand(nstep, 20, 3) coords_copy = coords.copy() cell = rand(nstep, 3, 3) c1 = np.array([np.dot(coords[ii,...], np.linalg.inv(cell[ii,...])) for ii in \ range(nstep)]) c2 = _flib.cart2frac_traj(coords, cell) c3 = crys.coord_trans3d(coords, new=cell, old=num.extend_array(np.identity(3), nstep=nstep, axis=0)) assert (coords == coords_copy).all() assert np.allclose(c1, c2) assert np.allclose(c1, c3) assert c2.flags.f_contiguous
def test_frac2cart_traj(): nstep = 100 coords_frac = rand(nstep, 20, 3) coords_frac_copy = coords_frac.copy() cell = rand(nstep, 3, 3) c1 = np.array([np.dot(coords_frac[ii,...], cell[ii,...]) for ii in \ range(nstep)]) c2 = _flib.frac2cart_traj(coords_frac, cell) c3 = crys.coord_trans3d(coords_frac, old=cell, new=num.extend_array(np.identity(3), nstep=nstep, axis=0)) assert (coords_frac == coords_frac_copy).all() assert np.allclose(c1, c2) assert np.allclose(c1, c3) assert c2.flags.f_contiguous
def test_dist_traj(): natoms = 10 nstep = 100 cell = rand(nstep, 3, 3) stress = rand(nstep, 3, 3) forces = rand(nstep, natoms, 3) etot = rand(nstep) cryst_const = crys.cell2cc3d(cell, axis=0) coords_frac = np.random.rand(nstep, natoms, 3) coords = crys.coord_trans3d(coords=coords_frac, old=cell, new=num.extend_array(np.identity(3), nstep, axis=0), axis=1, timeaxis=0) assert cryst_const.shape == (nstep, 6) assert coords.shape == (nstep, natoms, 3) symbols = ['H'] * natoms traj = Trajectory( coords_frac=coords_frac, cell=cell, symbols=symbols, forces=forces, stress=stress, etot=etot, timestep=1, ) for pbc in [True, False]: # (nstep, natoms, natoms, 3) distvecs_frac = traj.coords_frac[:,:,None,:] - \ traj.coords_frac[:,None,:,:] assert distvecs_frac.shape == (nstep, natoms, natoms, 3) if pbc: distvecs_frac = crys.min_image_convention(distvecs_frac) distvecs = np.empty((nstep, natoms, natoms, 3)) for ii in range(traj.nstep): distvecs[ii, ...] = np.dot(distvecs_frac[ii, ...], traj.cell[ii, ...]) # (nstep, natoms, natoms) dists = np.sqrt((distvecs**2.0).sum(axis=-1)) assert np.allclose(dists, crys.distances_traj(traj, pbc=pbc))
def test_coords_trans(): natoms = 10 nstep = 100 cell = rand(nstep, 3, 3) cryst_const = crys.cell2cc3d(cell, axis=0) coords_frac = rand(nstep, natoms, 3) coords = crys.coord_trans3d(coords=coords_frac, old=cell, new=num.extend_array(np.identity(3), nstep, axis=0), axis=1, timeaxis=0) traj = Trajectory(coords_frac=coords_frac, cell=cell) assert np.allclose(cryst_const, traj.cryst_const) assert np.allclose(coords, traj.coords) traj = Trajectory(coords=coords, cell=cell) assert np.allclose(coords_frac, traj.coords_frac)
def test_dist_traj(): natoms = 10 nstep = 100 cell = rand(nstep,3,3) stress = rand(nstep,3,3) forces = rand(nstep,natoms,3) etot=rand(nstep) cryst_const = crys.cell2cc3d(cell, axis=0) coords_frac = np.random.rand(nstep,natoms,3) coords = crys.coord_trans3d(coords=coords_frac, old=cell, new=num.extend_array(np.identity(3), nstep,axis=0), axis=1, timeaxis=0) assert cryst_const.shape == (nstep, 6) assert coords.shape == (nstep,natoms,3) symbols = ['H']*natoms traj = Trajectory(coords_frac=coords_frac, cell=cell, symbols=symbols, forces=forces, stress=stress, etot=etot, timestep=1, ) for pbc in [True, False]: # (nstep, natoms, natoms, 3) distvecs_frac = traj.coords_frac[:,:,None,:] - \ traj.coords_frac[:,None,:,:] assert distvecs_frac.shape == (nstep, natoms, natoms, 3) if pbc: distvecs_frac = crys.min_image_convention(distvecs_frac) distvecs = np.empty((nstep, natoms, natoms, 3)) for ii in range(traj.nstep): distvecs[ii,...] = np.dot(distvecs_frac[ii,...], traj.cell[ii,...]) # (nstep, natoms, natoms) dists = np.sqrt((distvecs**2.0).sum(axis=-1)) assert np.allclose(dists, crys.distances_traj(traj, pbc=pbc))
def test_coords_trans(): natoms = 10 nstep = 100 cell = rand(nstep,3,3) cryst_const = crys.cell2cc3d(cell, axis=0) coords_frac = rand(nstep,natoms,3) coords = crys.coord_trans3d(coords=coords_frac, old=cell, new=num.extend_array(np.identity(3), nstep,axis=0), axis=1, timeaxis=0) traj = Trajectory(coords_frac=coords_frac, cell=cell) assert np.allclose(cryst_const, traj.cryst_const) assert np.allclose(coords, traj.coords) traj = Trajectory(coords=coords, cell=cell) assert np.allclose(coords_frac, traj.coords_frac)
def test_traj(): natoms = 10 nstep = 100 cell = rand(nstep,3,3) stress = rand(nstep,3,3) forces = rand(nstep,natoms,3) etot = rand(nstep) cryst_const = crys.cell2cc3d(cell, axis=0) coords_frac = rand(nstep,natoms,3) coords = crys.coord_trans3d(coords=coords_frac, old=cell, new=num.extend_array(np.identity(3), nstep,axis=0), axis=1, timeaxis=0) assert cryst_const.shape == (nstep, 6) assert coords.shape == (nstep,natoms,3) symbols = ['H']*natoms # automatically calculated: # coords # cell # pressure # velocity (from coords) # temperature (from ekin) # ekin (from velocity) traj = Trajectory(coords_frac=coords_frac, cell=cell, symbols=symbols, forces=forces, stress=stress, etot=etot, timestep=1, ) # Test if all getters work. for name in traj.attr_lst: print "test if getters work:", name traj.try_set_attr(name) assert getattr(traj, name) is not None, "attr None: %s" %name assert eval('traj.get_%s()'%name) is not None, "getter returns None: %s" %name print "test if getters work:", name, "... ok" aaae(coords_frac, traj.coords_frac) aaae(coords, traj.coords) aaae(cryst_const, traj.cryst_const) aaae(np.trace(stress, axis1=1, axis2=2)/3.0, traj.pressure) assert traj.coords.shape == (nstep,natoms,3) assert traj.cell.shape == (nstep,3,3) assert traj.velocity.shape == (nstep, natoms, 3) assert traj.temperature.shape == (nstep,) assert traj.ekin.shape == (nstep,) assert traj.nstep == nstep assert traj.natoms == natoms traj = Trajectory(coords_frac=coords_frac, symbols=symbols, cell=cell) aaae(coords, traj.coords) # Cell calculated from cryst_const has defined orientation in space which may be # different from the original `cell`, but the volume and underlying cryst_const # must be the same. traj = Trajectory(coords_frac=coords_frac, symbols=symbols, cryst_const=cryst_const) np.testing.assert_almost_equal(crys.volume_cell3d(cell), crys.volume_cell3d(traj.cell)) aaae(cryst_const, crys.cell2cc3d(traj.cell)) # extend arrays cell2d = rand(3,3) cc2d = crys.cell2cc(cell2d) traj = Trajectory(coords_frac=coords_frac, cell=cell2d, symbols=symbols) assert traj.cell.shape == (nstep,3,3) assert traj.cryst_const.shape == (nstep,6) for ii in range(traj.nstep): assert (traj.cell[ii,...] == cell2d).all() assert (traj.cryst_const[ii,:] == cc2d).all() traj = Trajectory(coords_frac=coords_frac, cryst_const=cc2d, symbols=symbols) assert traj.cell.shape == (nstep,3,3) assert traj.cryst_const.shape == (nstep,6) for ii in range(traj.nstep): assert (traj.cryst_const[ii,:] == cc2d).all() # units traj = Trajectory(coords_frac=coords_frac, cell=cell, symbols=symbols, stress=stress, forces=forces, units={'length': 2, 'forces': 3, 'stress': 4}) aaae(2*coords, traj.coords) aaae(3*forces, traj.forces) aaae(4*stress, traj.stress) # iterate, check if Structures are complete traj = Trajectory(coords=coords, symbols=symbols, cell=cell, forces=forces, stress=stress, etot=etot, timestep=1.0) for struct in traj: assert struct.is_struct, "st is not Structure" assert not struct.is_traj, "st is Trajectory" assert_attrs_not_none(struct) struct = traj[0] for attr_name in traj.attr_lst: if attr_name in struct.attrs_only_traj: msg = "tr[0] %s is not None" %attr_name assert getattr(struct,attr_name) is None, msg else: msg = "tr[0] %s is None" %attr_name assert getattr(struct,attr_name) is not None, msg # slices, return traj keys = traj.attr_lst[:] tsl = traj[10:80:2] assert tsl.nstep == traj.nstep / 2 - 15 assert_attrs_not_none(tsl, attr_lst=keys) tsl = traj[slice(10,80,2)] assert tsl.nstep == traj.nstep / 2 - 15 assert_attrs_not_none(tsl, attr_lst=keys) tsl = traj[np.s_[10:80:2]] assert tsl.nstep == traj.nstep / 2 - 15 assert_attrs_not_none(tsl, attr_lst=keys) assert tsl.is_traj # iteration over sliced traj tsl = traj[10:80:2] for x in tsl: pass for x in tsl.copy(): pass # repeat iter for i in range(2): cnt = 0 for st in traj: cnt += 1 assert cnt == nstep, "%i, %i" %(cnt, nstep) # copy traj2 = traj.copy() for name in traj.attr_lst: val = getattr(traj,name) if val is not None and not (isinstance(val, types.IntType) or \ isinstance(val, types.FloatType)): val2 = getattr(traj2,name) print "test copy:", name, type(val), type(val2) assert id(val2) != id(val) assert_all_types_equal(val2, val) assert_dict_with_all_types_equal(traj.__dict__, traj2.__dict__, keys=traj.attr_lst)
def test_traj(): natoms = 10 nstep = 100 cell = rand(nstep, 3, 3) stress = rand(nstep, 3, 3) forces = rand(nstep, natoms, 3) etot = rand(nstep) cryst_const = crys.cell2cc3d(cell, axis=0) coords_frac = rand(nstep, natoms, 3) coords = crys.coord_trans3d(coords=coords_frac, old=cell, new=num.extend_array(np.identity(3), nstep, axis=0), axis=1, timeaxis=0) assert cryst_const.shape == (nstep, 6) assert coords.shape == (nstep, natoms, 3) symbols = ['H'] * natoms # automatically calculated: # coords # cell # pressure # velocity (from coords) # temperature (from ekin) # ekin (from velocity) traj = Trajectory( coords_frac=coords_frac, cell=cell, symbols=symbols, forces=forces, stress=stress, etot=etot, timestep=1, ) # Test if all getters work. for name in traj.attr_lst: print("test if getters work:", name) traj.try_set_attr(name) assert getattr(traj, name) is not None, "attr None: %s" % name assert eval('traj.get_%s()' % name) is not None, "getter returns None: %s" % name print("test if getters work:", name, "... ok") aaae(coords_frac, traj.coords_frac) aaae(coords, traj.coords) aaae(cryst_const, traj.cryst_const) aaae(np.trace(stress, axis1=1, axis2=2) / 3.0, traj.pressure) assert traj.coords.shape == (nstep, natoms, 3) assert traj.cell.shape == (nstep, 3, 3) assert traj.velocity.shape == (nstep, natoms, 3) assert traj.temperature.shape == (nstep, ) assert traj.ekin.shape == (nstep, ) assert traj.nstep == nstep assert traj.natoms == natoms traj = Trajectory(coords_frac=coords_frac, symbols=symbols, cell=cell) aaae(coords, traj.coords) # Cell calculated from cryst_const has defined orientation in space which may be # different from the original `cell`, but the volume and underlying cryst_const # must be the same. traj = Trajectory(coords_frac=coords_frac, symbols=symbols, cryst_const=cryst_const) np.testing.assert_almost_equal(crys.volume_cell3d(cell), crys.volume_cell3d(traj.cell)) aaae(cryst_const, crys.cell2cc3d(traj.cell)) # extend arrays cell2d = rand(3, 3) cc2d = crys.cell2cc(cell2d) traj = Trajectory(coords_frac=coords_frac, cell=cell2d, symbols=symbols) assert traj.cell.shape == (nstep, 3, 3) assert traj.cryst_const.shape == (nstep, 6) for ii in range(traj.nstep): assert (traj.cell[ii, ...] == cell2d).all() assert (traj.cryst_const[ii, :] == cc2d).all() traj = Trajectory(coords_frac=coords_frac, cryst_const=cc2d, symbols=symbols) assert traj.cell.shape == (nstep, 3, 3) assert traj.cryst_const.shape == (nstep, 6) for ii in range(traj.nstep): assert (traj.cryst_const[ii, :] == cc2d).all() # units traj = Trajectory(coords_frac=coords_frac, cell=cell, symbols=symbols, stress=stress, forces=forces, units={ 'length': 2, 'forces': 3, 'stress': 4 }) aaae(2 * coords, traj.coords) aaae(3 * forces, traj.forces) aaae(4 * stress, traj.stress) # iterate, check if Structures are complete traj = Trajectory(coords=coords, symbols=symbols, cell=cell, forces=forces, stress=stress, etot=etot, timestep=1.0) for struct in traj: assert struct.is_struct, "st is not Structure" assert not struct.is_traj, "st is Trajectory" assert_attrs_not_none(struct) struct = traj[0] for attr_name in traj.attr_lst: if attr_name in struct.attrs_only_traj: msg = "tr[0] %s is not None" % attr_name assert getattr(struct, attr_name) is None, msg else: msg = "tr[0] %s is None" % attr_name assert getattr(struct, attr_name) is not None, msg # slices, return traj keys = traj.attr_lst[:] tsl = traj[10:80:2] assert tsl.nstep == traj.nstep / 2 - 15 assert_attrs_not_none(tsl, attr_lst=keys) tsl = traj[slice(10, 80, 2)] assert tsl.nstep == traj.nstep / 2 - 15 assert_attrs_not_none(tsl, attr_lst=keys) tsl = traj[np.s_[10:80:2]] assert tsl.nstep == traj.nstep / 2 - 15 assert_attrs_not_none(tsl, attr_lst=keys) assert tsl.is_traj # iteration over sliced traj tsl = traj[10:80:2] for x in tsl: pass for x in tsl.copy(): pass # repeat iter for i in range(2): cnt = 0 for st in traj: cnt += 1 assert cnt == nstep, "%i, %i" % (cnt, nstep) # copy traj2 = traj.copy() for name in traj.attr_lst: val = getattr(traj, name) if val is not None and not (isinstance(val, int) or \ isinstance(val, float)): val2 = getattr(traj2, name) print("test copy:", name, type(val), type(val2)) assert id(val2) != id(val) assert_all_types_equal(val2, val) assert_dict_with_all_types_equal(traj.__dict__, traj2.__dict__, keys=traj.attr_lst)
def test_coord_trans(): #----------------------------------------------------------- # 2D #----------------------------------------------------------- c_X = rand(20,3) # basis vecs are assumed to be rows X = rand(3,3)*5 Y = rand(3,3)*3 # transform and back-transform c_Y = coord_trans(c_X, old=X, new=Y) c_X2 = coord_trans(c_Y, old=Y, new=X) aaae(c_X, c_X2) # simple dot product must produce same cartesian results: # X . v_X = I . v_I = v_I X = np.identity(3) Y = rand(3,3)*3 c_X = rand(20,3) c_Y = coord_trans(c_X, old=X, new=Y) # normal back-transform c_X2 = coord_trans(c_Y, old=Y, new=X) # 2 forms w/ dot(), assume: basis vecs = rows of X and Y c_X3 = np.dot(c_Y, Y) c_X4 = np.dot(Y.T, c_Y.T).T aaae(c_X, c_X2) aaae(c_X, c_X3) aaae(c_X, c_X4) # some textbook example # v_I = np.array([1.0,1.5]) I = np.identity(2) # basis vecs as rows X = sqrt(2)/2.0*np.array([[1,-1],[1,1]]).T Y = np.array([[1,1],[0,1]]).T # "identity" transform aaae(coord_trans(v_I,I,I), v_I) # v in basis X and Y v_X = coord_trans(v_I,I,X) v_Y = coord_trans(v_I,I,Y) aaae(v_X, np.array([1.76776695, 0.35355339])) aaae(v_Y, np.array([-0.5, 1.5])) # back-transform aaae(coord_trans(v_X,X,I), v_I) aaae(coord_trans(v_Y,Y,I), v_I) # higher "x,y,z"-dims: 4-vectors c_X = rand(20,4) X = rand(4,4)*5 Y = rand(4,4)*3 c_Y = coord_trans(c_X, old=X, new=Y) c_X2 = coord_trans(c_Y, old=Y, new=X) aaae(c_X, c_X2) #----------------------------------------------------------- # 3D #----------------------------------------------------------- # x,y,z case c_X = rand(20,3,10) X = rand(3,3)*5 Y = rand(3,3)*3 c_Y = coord_trans(c_X, old=X, new=Y, axis=1) c_X2 = coord_trans(c_Y, old=Y, new=X, axis=1) aaae(c_X, c_X2) c_X = rand(20,10,3) c_Y = coord_trans(c_X, old=X, new=Y, axis=-1) c_X2 = coord_trans(c_Y, old=Y, new=X, axis=-1) aaae(c_X, c_X2) c_X = rand(3,20,10) c_Y = coord_trans(c_X, old=X, new=Y, axis=0) c_X2 = coord_trans(c_Y, old=Y, new=X, axis=0) aaae(c_X, c_X2) # 3d, higher "x,y,z"-dims, i.e. 4-vectors: trajectory of 5 atoms, 10 steps, # "4d-coordinates" c_X = rand(20,4,10) X = rand(4,4)*5 Y = rand(4,4)*3 c_Y = coord_trans(c_X, old=X, new=Y, axis=1) c_X2 = coord_trans(c_Y, old=Y, new=X, axis=1) aaae(c_X, c_X2) #----------------------------------------------------------- # ND #----------------------------------------------------------- # arbitrary collection of 4-vectors c_X = rand(20,4,10,8) X = rand(4,4)*5 Y = rand(4,4)*3 c_Y = coord_trans(c_X, old=X, new=Y, axis=1) c_X2 = coord_trans(c_Y, old=Y, new=X, axis=1) aaae(c_X, c_X2) #----------------------------------------------------------- # special case 3d #----------------------------------------------------------- # Note that axis=1 is always the xyz-axis (length 3) if the timeaxis # (length 10) would be removed from all arrays (2d case then). c_X = rand(20,3,10) X = rand(3,3,10)*5 Y = rand(3,3,10)*3 c_Y = coord_trans3d(c_X, old=X, new=Y, axis=1, timeaxis=2) c_X2 = coord_trans3d(c_Y, old=Y, new=X, axis=1, timeaxis=2) aaae(c_X, c_X2) c_X = rand(20,10,3) X = rand(3,10,3)*5 Y = rand(3,10,3)*3 c_Y = coord_trans3d(c_X, old=X, new=Y, axis=1, timeaxis=1) c_X2 = coord_trans3d(c_Y, old=Y, new=X, axis=1, timeaxis=1) aaae(c_X, c_X2) c_X = rand(10,20,3) X = rand(10,3,3)*5 Y = rand(10,3,3)*3 c_Y = coord_trans3d(c_X, old=X, new=Y, axis=1, timeaxis=0) c_X2 = coord_trans3d(c_Y, old=Y, new=X, axis=1, timeaxis=0) aaae(c_X, c_X2)